Misunderstanding
by YellowShadess
Summary: Booth and Brennan have a few misunderstandings between them thanks to Angela. AU set between 6x01 and 6x09
1. Chapter 1

**Hey guys! YellowShadess here with a new story! Its surrounds a few misunderstandings between Booth and Brennan. Its pretty AU. Set between 6x01 and 6x09. I hope you enjoy it!**

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"Angela! How could you do that!"

"Because sweetie. I knew you wouldn't tell him yourself. You just needed a little push."

"But Ang I don't think Booth is going to appreciate a letter "professing my love to him" just laying on his office desk. I would talk to him in person about this; I would never do that so why did you?" Brennan asked with her hands on her hips. The pair stood in Angela's office discussing last nights festivities and what Angela had just done. Angela rolled her eyes,

"You are never going to tell him. He's going to run off with Baghdad Barbie and he will never know how you feel." Brennan shook her head

"He is happy with her. He does not need to know my feelings for him. He's happy and thats all I care about."

"But sweetie-" a loud roar boomed through the lab. Brennan and Angela peaked out of the office to see what the commotion was about.

"BONES! WHERE ARE YOU?" Brennan went out of the office and found his partner standing with his hands on his hips. Angela walked out behind her and stood in her office door.

"Booth. Whats wrong?" He looked at her with wide angry eyes,

"Really? Whats wrong? Well, first I ran out of coffee, then I was late to work and oh yeah, my partner decided to leave a letter on my desk professing her love for me!" He held up a crumpled piece of paper to her face. She gaped at it and spoke,

"Booth. You don't understand-" He cut her off abruptly,

"I don't understand?! No Bones. I do understand. I understand that you don't know what love truly is. I mean really? A letter? You didn't even have the decency to talk to me face to face. God no! You did what you always do and make everything cold and rational. It's all printed all nice on crisp white paper just saying that you love me. Whats the matter Bones? Was I not worth your letterhead? Let me tell you something. I am happy with Hannah. She is the best thing that has happened to me in a while. And now this? Where was this last year in front of the Hoover huh? You know what? never mind about that. I'm just here to tell you that this letter means nothing to me. I am happy and your words mean nothing. So I hope you're happy." He crumpled up the letter into a ball and stormed out of the lab, leaving Brennan standing in the middle of the lab with her mouth gaped open and tears in her eyes. She looked around and saw that everyone in the area had stopped working and were all fixated on her.

"Sweetie?" Angela asked quietly. She had joined next to Hodgins who came out of his office when he started to hear the yelling. Brennan whipped her head around and looked at Angela and Hodgins,

"What did I tell you Angela?" She ran into her office, grabbed her stuff and quickly made her way out of the lab.

"Okay people. Back to work and NO GOSSIP." Cam bellowed out from on top of the platform. She walked towards Angela and Hodgins with wide eyes,

"Oh my god." Cam said. Hodgins nodded and spoke,

"That was intense. I don't think I ever saw Booth rip into Dr. B like that." A sob emitted from Angela. She hugged her stomach and put a hand over her mouth. Hodgins saw his wife's distress and went to her side, "Baby, whats wrong?" She shook her head,

"It's my fault. Bren and I were hanging out last night when she admitted her feelings about Booth to me. I told her se should tell him but she refused. So I decided to give her a nudge. I wrote what she said down and wrote him the letter. I left it on his desk earlier this morning." Both Cam and Hodgins sighed,

"Angie, why would you do that?" Hodgins asked calmly but with a bit of edge in his voice,

"Because she deserves to be happy. She deserves everything she dreams about and I was trying to give that to her. I didn't think he would react like that though." Hodgins hugged his hormonal wife and soothed her. Cam rubbed her forehead and spoke,

"Where is Dr. Brennan right now?" Hodgins shrugged,

"She ran out of here right after Booth left. She didn't say where she was going but I can't imagine she's be back today." Cam nodded and spoke once more,

"Okay. I'm going to see about getting in touch with Brennan. Angela calm down and relax. Hodgins take care of her. I'll let you know if I talk to her." Cam left the couple to themselves and went to her office. She dialed Brennan's phone number but was sent straight to voicemail. Damn, she turned her phone off. She tried her house number was got nothing as well. She tried Booth but was sent to voicemail after 2 rings. She sent Brennan a text message and email requesting her to call the lab so they all know she's fine. Cam didn't have high hopes for that though. The group decided to get back to work and let the partners cool off.

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 _Two hours later..._

Booth carefully walked into the lab. It had been a few hours since he blew up on his partner and he wanted to talk to her. He walked in and saw that everyone was staring at him. He picked up the pace to her office when he saw that the door was closed and the lights were off. He made his way to Cam's office and knocked lightly,

"Hey Cam? Where's Bones?" He asked softly. She looked up at him with annoyed confusion in her eyes,

"Are you really going to stand there and ask me where Dr. Brennan is?" He nodded hesitantly. She shook her head in anger. "I don't know Booth. After your little chat where you ripped her apart she took her stuff and left. I can't reach her anywhere." Both exhaled deeply,

"I-I'm sorry." He said while looking at his shoes. She looked at him

"I'm not the one you should be apologizing to. You should be out there searching for your devastated partner and making things right." He was about to leave when she stopped him,

"Before you go running all over DC looking for her I think you should go talk to Angela. I think she will give you some insight you'll want to hear." She turned back to her work as Booth made his way to the artists office. He saw Angela sitting on her couch with her hands on her round belly, admiring her unborn child. She didn't notice his presence until he cleared his throat. She looked up at him with tear streaks down her face. She wiped the tears away and looked at him with disgust,

"What Booth? You here to rip into me too?" He sighed and spoke,

"No. I know I messed up big time. Cam told me that Bones isn't here so I was going to go find her. She also told me to come here before I left; something about some important insight?" A sob came from the artists mouth and startled Booth. She controlled her emotions and spoke,

"Bren didn't write the letter I did." Booth looked at her with wide eyes,

"What? Why would you do that?" He couldn't believe it,

"Because she needs to be happy and you deserve to know how she feels. She told me last night that she is in love with you. She told me about how she turned you down last year and how she regrets it everyday. I knew she would never tell you because she really believes that you're happy with Hannah so I wrote the letter and put it on your desk this morning. I didnt expect you to react like that though Booth what the hell was that?" She asked with her arms crossed against her chest. He shrugged his shoulders and dropped to the couch,

"I don't even know Ange. When I saw the letter I was so hurt. I didn't think Bones would ever do that to me. She always talked to me about her problems and what she feels but since we came back from our trips I felt us grow apart and when I saw this I saw red because this showed me that she didnt care anymore. Clearly thats not the case though is it?" He looked angrily at Angela,

"I'm sorry. I just want her to be happy and I know that both of you would be so happy if you just dropped this bullshit and get together. I really messed up on this one and I am very sorry." She sat next to him and sighed, He sat back on the couch and spoke,

"How was she?" Angela shook her head and took a deep breath,

"She looked... mortified. You attacked her character Booth, you attacked her feelings in front of the entire lab. She looked like she was holding back her tears when she bolted from here. I don't know where she is." She knew his next question. He nodded and rubbed his face. He really messed up now. He needed to fix things.

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 **I hope you enjoyed this. I will post chapter 2 soon. -J.A.**


	2. Chapter 2

**Hey guys! I'm happy that everyone enjoyed the first chapter! I hope I can get these chapters up ASAP so fingers crossed! Here is chapter 2**

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Brennan slammed her apartment door shut in anger. She furiously wiped the tears off her face as more came soaring down. She dropped her bag on the floor and shrugged her coat off. She looked around and willed herself to stop crying. His words still spun in her head, _you make everything cold and rational. Your words mean nothing to me._ A sob escaped her lips as more tears came to her eyes. She knew he moved on but his words struck her like a knife.

" _Well, I guess thats it then."_ She thought. She took her shoes off and made her way to her bedroom. She changed into sweats and made her way to her couch. She had no desire to go anywhere or talk to anyone so she placed herself on her couch and write her novel. Today was her day to sit down and really work on her latest book today so she used that opportunity to get her mind off of Booths mean words; Although now she had some rerouting to do to her ideas. She felt the vibrations of her phone and checked it out. It was the Jeffersonian calling. She clicked ignore and shut her phone off completely. A few minutes go by and her house phone begins to ring as well. She ignored that too and went along with her writing. She wanted no contact with the outside world for the day.

Brennan sat for a while, loosing track of time as she pumped out chapter after chapter of the adventures of Kathy and Andy. Although this time she was finding new ways to end the partnership between her characters. Her secret muse was no longer available so she worked on ending the dynamic or even the series all together. As she was writing a chapter in which Andy breaks Kathys heart a few bangs erupted from her door. The bangs jolted her from her thoughts. She kept quiet in hopes that the intruder would leave.

"Bones?" She felt the color drain from her face when she heard the nickname and the voice that often paired with it. She sat perfectly still in hopes that he wouldn't hear her. "Open up. I'm sorry please we need to talk." She heard more knocks as tears once again ran down her face leaving behind two twin trails. She put a hand over her mouth in an effort to muffle the sobs that threatened to come up. She heard the clicking of a key and silently thanked god that she changed her locks. Brennan wasn't ready to talk to him; she didn't know if she would ever be ready to face him. She heard footsteps walk away from the door. One peak out her peep hole told her that he had left. Probably to go search for her somewhere else.

The attempted confrontation forced her out of her writing session and made her realize that she should eat. Going out and grabbing something was on her mind until she realized that she could bump into him or she would come back to her apartment and he would be there. Maybe she would forgo food for now.

Brennan couldn't get Booth out of her mind. For the rest of the day she tried to keep herself preoccupied with writing, email checking and grading papers but her thoughts only consisted of the harsh words that came from her partner and all the looks she received from the people at the lab. She saw the email from Cam and decided to email her back letting her know that she was fine and would be back in the lab tomorrow morning. She apologized for her absence and sent the email. She was sitting on her couch pretending to grade papers when she heard knocks again. She watched the door in a mixture of horror and anger. She knew who was there; she knew he would come back,

"Bones, I know you're there. I tracked your phone. I don't care how long it'll take I am going to stay here until you come out. I'm so sorry Bones. Please open the door so we can talk?" He asked gently. The tears welled in her eyes once more but she willed them away. She sat still until she heard a light thump coming from the hall. She lightly made her way to the door and looked out the peephole. She saw him sitting on the floor with his head in his hands. With her forehead resting up against her door, eyes shut and tears running down her face she debated on what to do; open the door and talk to him? or let him sit there until he gets tired and leaves?..

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Booth walked out of the lab and went straight to her apartment on his first stop to finding her. Her car was parked in her usual spot so that was a good sign. He walked up to the door and knocked loudly,

"Bones. Open up. I'm sorry please we need to talk." Nothing. He knocked once more and pressed his ear up to her door. He didn't hear any movement. He pulled out his keys and found the one that opens her door. He pushed it into the lock and tried to turn it but it didn't work. Weird. He made sure it was the right key and tried again. It wouldn't open. Did she change her locks? When did she change her locks? Booth decided to figure that out later and went on to other stops.

The coffee cart. No

Wong Foos. No

The Diner. No

The Jeffersonian gardens. No

Even the lab once more. No.

She was nowhere to be found. He asked around these areas to see if she had been seen and no one saw her today. He started to get nervous. He went back to the FBI and put a track on her phone. Her last known location was at her apartment a few hours ago. Booth decided to go back to her apartment in an attempt to talk to her. Once he arrived back at her door he knocked again,

"Bones I know you're there. I tracked your phone. I don't care how long it'll take I am going to stay here until you come out. I'm so sorry Bones. Please open the door so we can talk?" No movement was made so he took off his jacket and took a seat against the wall across from her door and waited. He put his head in his hands and thought about what he was going to say to her. He didn't know how he was going to fix this but he was going to try his hardest. He was so caught up in his thoughts he didn't notice the sound of her lock turning and the door opening slightly...

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 **I hope I dont take too long for the next chapter. -J.A.**


	3. Chapter 3

**Hey guys! I hope you enjoyed chapter 2. Here is chapter 3!**

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Brennan opened her door slightly and saw that the he didn't hear her. She stood there watching him get lost in his own thoughts. She debated on what to say to him but then decided. She quietly opened the door a little more and spoke,

"You should leave Booth." He looked up and saw her standing there in her t shirt and sweats. It wasn't until he got up off the floor that he noticed the tear tracks on her face,

"Bones-" She cut him off,

"You should leave Booth. Go home." He took a step closer to her door as she began shutting her door. His big hand stopped it,

"Bones please. I need to talk to you." She shook her head and stopped the tears,

"You've said enough. Just go home to Hannah, she's probably waiting for you." She pushed her hardest on the door and got it to close on him. Her words left him stunned enough to let up on the door. The sadness and anger in her eyes made his breath hitch. He was kicking himself for being the person to bring those emotions to her eyes. Once he gained his voice back he spoke loudly enough for her to hear through the door,

"I'm not leaving Bones. For as long as it takes I will wait here so we can talk." When he realized that she would not be opening the door he resumed his spot on the floor and got caught in his thoughts once more,

Hannah. he hasn't thought about her all day even after he yelled at his partner about loving her. What was he going to do? He was going to try his hardest to gain back her trust.

He sent a quick text to Hannah saying that he was working late and might not be home. Tossing his phone to the side and putting his head in his hands once more Booth got lost in his thoughts. Thoughts about his amazing partner that was always there for him even when he was a bastard to her. It was like the events today have made him realize that he has been treating her badly since their return. Leaving her behind, not going out to eat with her, leaving her with the paperwork just so he can go have sex with his girlfriend. He groaned at his actions and shook his head at himself.

He sat there for a long time lost in his thoughts. He didnt know how long he had been sitting there when he was jolted from his thoughts hearing the ding of the elevator and heavy footsteps. A woman blew passed him and went up to Brennan's door,

"Bren. Are you there? Please open up I'm sorry." He recognized the woman as Angela, their resident artist and instigator.

"Angela." She turned around and saw who had called her name,

"Booth. How long have you been here?" He shrugged.

"A few hours. She's in there but she won't open the door." Angela sighed in defeat and took a seat next to the agent,

"What am I going to do?" Booth shrugged his shoulders and sighed,

"Try talking to her? Thats what I'm doing. I'm going to wait here for as long as I have to." She nodded,

"I'll wait with you." He shook his head,

"No you're not." She was about to argue when he said more, "I don't know how long I'm going to be sitting here. Probably all night. You're five months pregnant you can't sit on this floor. Go home. My guess is that she's going to go to work tomorrow so you can catch her there." Angela nodded in agreement. Booth got to his feet and helped Angela up and walked her to the elevator. They said their goodbyes and Booth made his way back to his stop and spent the rest of the night waiting for her to open the door. She never did.

His phone said it was midnight so he made a makeshift pillow out of his jacket and laid down on the floor. He was determined to talk to her so he wasn't leaving. He knew he probably wasn't sleeping that night but he didn't care. Around a half hour later he was startled by unlocking sounds and a door being thrown open,

"Absolutely not. You are not sleeping on the floor." There stood his partner; still in the same clothes as before with one hand on her hip and the other on the door ready to slam it at any moment. He jumped up quickly,

"Bones-" She cut him off,

"No Booth. You are not sleeping on the floor in my hallway." He stood his ground,

"Well, I'm not leaving until we sit down and talk about what happened today." She shook her head,

"I'm not talking to you about this right now." He leaned up against the wall,

"I'm not leaving then." She let go of her door and stomped up to him and got as close as possible. She raised a finger up to his face and spoke in a low angry voice,

"You listen to me Seeley Booth. You need to go home and leave me alone. " he tried it interrupt her but she pushed her finger closer to his face and continued, "no, you cannot sleep on this floor; it is not good for your back. You need to go home. I am not ready to see you; I am not ready to talk to you. Just me standing here talking to you is hurting me. When I am ready I will come to you but please leave me alone right now." She stared into his brown eyes for a brief moment, dropped her hand, went back into her apartment and shut the door on a defeated Booth. The noble thing to do would be to let her be for now and catch her when she's ready. He decided that's the best option for now. He will talk to her though. He'll stop by the lab tomorrow. He grabbed his jacket and slumped his way to his car and all the way home.

Sleep didn't come easy to Booth. He came home to find Hannah asleep. Silently thanking god he got changed and made a makeshift bed on the couch for the night. He laid awake thinking about the beautiful anthropologist that he had hurt deeply.

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 **Hope you enjoyed it! I'll be back soon with chapter 4 -J.A.**


	4. Chapter 4

**Hey guys. I hope you liked the last chapter! Here is chapter 4**

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Brennan waited by the door to make sure Booth actually left. When she saw him gather is stuff off the floor and hesitantly left her building, she felt the tears come but she willed them away. She was done crying over him. She made sure her doors were locked and went straight to bed for a night of restless sleep.

The morning came too fast for Brennan and not fast enough for Booth. The moment he saw the sun come up he jumped off the couch and got ready. He needed to talk to his partner so he decided that he would go to the lab and wait for her. He did his best to make sure he didn't wake Hannah while he was getting dressed. By the time he was at the lab it was 7 am. He expected her to be there by now but also wasn't surprised when he saw that her office was still closed. He walked past Angela's office and saw the artist in her office sitting at her desk,

"Angela?" He walked up to her door and spoke, "You're here early." She looked up and gave him a sad smile,

"Yeah, I was hoping to beat Bren here to talk. Looks like I did. What are you doing here?" He shrugged,

"Same here." She nodded,

"How was sleeping on the floor?" He took a deep breath and spoke,

"Actually, I was getting ready to sit there all night but then Bones came out and yelled at me go home. She told me that she isn't ready to talk to me and that sleeping on the floor isn't good for my back." Angela smiled at her friends consideration,

"I'm not surprised she made you leave. She knows how bad your back is." He shook his head,

"Can you believe that? Even when I was a bastard to her she still cared for me. *signs heavily* Why did I make such a mess of things Angela?" He took a seat on her couch and put his head in his hands. Angela took a seat next to him and rested a supportive hand on his shoulder,

"I don't know Booth. Brennan told me about last year in front of the FBI building. She told me she didn't think things would change but it seems like it did." Booth shook his head and pressed his face harder into his hands in an effort to stop the tears,

"It was me Ange. I was so hurt by her rejection I thought that pulling away would be best. I was an idiot for thinking that because she continued to be the amazing woman and partner she is and all I could do was ignore her and try to convince myself that I had moved on." Angela sat there and soothed the agent's sadness. Little did the pair know that the aforementioned Bones/Bren has shown up and had heard what her partner had said. Her thoughts fought with each other about what she should do,

 _Talk to him. You know you miss him and he couldn't have meant what he said._

 _Couldn't have meant what he said?! If he didn't mean it then why did he say it?_

 _Talk to him to find out._

 _I don't think I'm ready._

 _Will you ever be ready?_

Brennan was pulled from her thoughts when she sensed movement. She quickly made her way to her office, grabbed her lab coat and made her way down to Bone Storage. She knew limbo would help her escape her best friend and partner from talking to her. She saw Booth leave her alone last night but she knew he wouldn't stay away for long. Evidence being his words to Angela and his presence this morning.

Angela won't stay away either. She is going to realize where she is and go searching for her. She just hoped that limbo would hide her for a while. Brennan knew that she couldn't stay away from Cam. She had to go speak to her and make sure she knows she is present for the day. After sneaking up the stairs and seeing that Booth was sitting in her office, most likely waiting for her, and Angela was out of side, most likely in either her office or Hodgins'. She quickly made her way to Cam's office.

"Dr. Saroyan." Brennan knocked on the door, getting the attention of the pathologist. Cam lifted her head and greeted her visitor,

"Dr. Brennan. I'm glad that you're back." Brennan gave her boss a small smile,

"Yes, I apologize for my absence yesterday-" Cam cut her off,

"No need to apologize. I understand completely. Booth is sitting in your office. He came by just before you walked in." Brennan nodded,

"Yes, I saw him sitting on my couch. I am currently down in Bone Storage working on the identification of a World War II soldier so if you need me I will be down there." Cam nodded and stopped Brennan from leaving,

"What about if someone else needs you?" she prodded. Brennan took a deep breath and spoke,

"If someone needs me for an anthropological viewpoint I will be available. If it is personal it can wait." Giving the answer to the silent question Cam asked, _What if Booth or Angela are looking for you?_ As Brennan was leaving she almost bumped into their resident artist. Brennan was caught off guard,

"Bren." Angela sighed in relief. Brennan nodded,

"Angela." She went out of her way not to make eye contact. "You know where I will be Dr. Saroyan." Before Angela could stop her Brennan made her way out of Cams office and quickly went back down to Bone Storage. Angela stood in Cam's office with her mouth gaped open,

"Where is she?" Cam straightened up and spoke,

"If you need Dr. Brennan for her professional opinion I will gladly call her for you." Angela put her hands on her hips and spoke in frustration,

"Why won't you tell me where she is?" Cam shook her head,

"Because she asked me to. Yesterday was horrifying to her, if she wants her privacy I'm going to give it to her." Angela nodded,

"I know where she is." Cam shrugged her shoulders,

"I didn't tell you where she is. if you find her then good for you." Angela stomped out of her office and to Brennan's office to find Booth.

"Booth. She's here." His head shot up at the mention of his partner,

"Where is she?" Angela shrugged,

"I dont know. Cam does. I tried to pretend that I know where she is so she would give it up but she didn't. She can't be far though." Angela took a seat next to Booth,

"Lets think. Where would she be to get away from talking to people?" The pair brainstormed and made the same conclusion,

"Limbo."

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 **Hope you like this chapter! I'll be back soon with chapter 5 -J.A.**


	5. Chapter 5

**Hey guys! I hope you liked the last chapter. Here is chapter 5!**

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Both Booth and Angela got up at the same time and were about to make were about to make their way down to Bone Storage when Booth stopped them,

"Wait, we can't both go down there at the same time. We'll just bombard her enough to make her close up more." Angela nodded in agreement,

"So... who goes first?" Booth sighed and spoke,

"I saw her yesterday so you can go down there now. I'll try to catch her later." Booth knew how important Brennan was to Angela and how important it is for her to get her apology in. Booth decided to follow Brennan's orders for a little longer. Angela gave Booth a grateful smile and thanked him. He watched her walk away in search for his partner. He decided to make his way to work and hopefully catch her at lunch.

Angela made her way quietly down the stairs that lead to 'Limbo', a storage area in the basement that holds the bones of thousands of lost souls. Brennan was often down in Limbo when she was feeling bad or wanted to escape reality. It was only fitting that Angela found her best friend bent over a skeleton with her back towards the door after the day she had yesterday. Angela made sure not to frighten her friend,

"Bren?" Brennan didn't look up, "Bren. Can I talk to you?" Brennan sighed a little,

"I'm busy Angela." Angela sighed sadly,

"Please? I really need to talk to you." Brennan shook her head and kept her back turned,

"If this is about the events of yesterday I am not in the mood to discuss it so please leave me to my work." Angela wouldn't back down,

"Bren, I need you to know how sorry I am. I didn't do what I did to hurt you. I did it so you could be happy." Brennan whipped around and looked at the artist,

"How was that going to make me happy? How was confessing MY feelings to MY partner going to make me happy? You had no right Angela. None at all. You may have just cost me one of the best relationship I've ever had because you can't mind your business. I know Booth is sorry and he claims that he didn't mean what he said but I don't know if I can look at him the same way anymore. I'm going to tell you what I told Booth. Leave me alone. I will come to you when I am ready. For now though, leave me alone." Without a look back Brennan turned back to her work and left Angela standing there stunned. The artist attempted to gather herself before going back to the main lab,

"I'm sorry." Brennan heard the tears in her voice and it hurt her. She knew she shouldn't feel bad for what she said for Angela but she knew the artist was only looking out for her well being. She needed to be told how Brennan felt though. Brennan always took pride in her honesty; especially in times like these.

Angela made it just in time to her office to totally breakdown from what Brennan had just said to her. She couldn't believe thats how her best friend thought of her and she was sickened with herself, As she dropped to her couch to calm down Hodgins walked in,

"Ange do you have the notes on the Briggs case? I thought I had them-" He cut himself off when he saw how distraught his wife was sitting on her couch,

"Angie, What's wrong?" Angela shook her head and out her head on his shoulder,

"I just saw Brennan. She said she didn't want to talk to me and that when she's ready to talk she will find me." The tears began once more, "She told me I might have just ruined her and Booth's relationship. How could I do that Hodgie? I ruined everything for her." She started to sob once more. Hodgins took his wife into an embrace and held her as she cried.

"Angie, everything is going to be Okay." She shook her head,

"No it won't be. She's going to hate me forever. She has every right to anyways." Hodgins shook his head and spoke,

"You know thats not true. Brennan just needs some time to herself. She'll come around soon. Just give her time." Angela hesitantly nodded at her husbands words. After a while of them just sitting together on her couch they went back to work.

Soon lunch rolled around and Booth found himself back at the lab. He gave Angela the morning to talk to Brennan and now he was determined to at least get her for lunch. He saw that her office was still empty so he went to see if she was in bone storage. he walked down the steps and saw her hunched over the examination table. He didn't know that she had not moved, except to get new remains, since this morning. He stopped at the bottom of the steps and made his presence known.

"Hey Bones. You hungry?" He couldn't see her face but her expression was one of annoyance,

"No. I'm not hungry." She said somewhat softly. In an effort to break the tension Booth cracked a joke,

"Oh, come on Bones. You gotta eat." She shook her head,

"I don't have much of an appetite right now. If you'll excuse me I need to return to these remains." He shook his head,

"Bones, please" She turned around and spoke,

"Booth. What did I say last night?" He knew what she said but he didn't want to repeat it, "I told you to leave me alone. I told you that when I was ready I'll come to you. It seems like you don't listen so I will say it once more. Booth, leave me alone. This is not something you can fix in a day. You and Angela have to leave me alone." She turned back to her remains and left Booth standing there.

"Bones..." He jumped when he heard the slamming of her fists on the side of the table,

"Do I have to leave? Do I have to leave the lab to get away from you two? I don't want to do that but if thats the case then I will go." Booth shook his head,

"No. Don't leave. I will go." She didn't turn back to watch him leave. He went up the stairs and out of the lab. She felt tears well in her eyes. She wiped them away and continued with her work.

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 **I hope you enjoyed this** **chapter! I'll be back soon. -J.A.**


	6. Chapter 6

**Hey guys! I'm glad you enjoyed the last chapter! the story will conclude soon I'm just figuring out when that'll be. Here is chapter 6**

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The day dragged on for the team.

In the many years Brennan worked at the Jeffersonian she never wanted the work day to end... besides today. She kept herself holed up in limbo and was thankful that no cases came up. The minute it hit 4pm she gathered her things and made her way home. She dodged another attempt at speaking from Angela and went home. Brennan's emotions were conflicting with each other currently; on one hand she felt guilty for treating Angela and Booth the way she has been but on the other hand she was still angry and hurt by them. All she wanted was peace from this whole ordeal.

Booth sat in his office and pretended to be doing work. He couldn't get his mind off of his heartbroken partner. The cruel words circled in his mind, a reminder of the pain and sadness he gave to his Bones. He didn't know what to do. After reviewing the words he spoke he concluded that everything he said was bullshit. He valued every word that came out of her mouth. He didn't love Hannah like he said he did and he didn't move on from Brennan. He was still in love with her and it terrified him that he might have just ruined their relationship or any future they had together. At 4 he finally gave up on work and made his way home. He needed to figure out a way to fix things between him and Brennan. He would wait for her to come to him like she asked but he wanted to fix things soon. He wouldn't push her though.

Angela sulked around her office all day. She still hated herself for what she had done. Everything Brennan had said to her was true, she always butts into peoples business she didn't belong in. All she wanted was for her best friend to find love with the man she was in love with but she messed that up big time. Hodgins tried a few times to cheer her up, he even suggested going to talk to Brennan for her but she said she would honor Brennan's wishes and wait for her to be ready. When that'll be she didn't know but she would wait for her. 4pm rolled around and the small family decided to head home for the night. Angela make an attempt to talk to Brennan but she just ducked away.

* * *

Brennan grabbed take out from the diner and went home for a night of solitude and work. She might return to the lab later on in the night.

Angela went home and went straight to bed. Hodgins worried about his wife. He grabbed her some food and made his way to their bedroom to keep her company.

Booth made his way home. He sulked into his apartment, hung his jacket on the coat hanger and went to his bedroom. He saw Hannah sitting on the bed working on a story. A sense of dread pushed its way into his mind. Hannah was here with him but he didn't want her to be. He grew angry with her. _This is all her fault. Don't be an asshole Seeley, this is entirely your fault._ His anger went away when she looked at him and smiled. They greeted each other with a small kiss.

"Hi Seeley, how was work?" He inwardly shuttered, instantly thinking of the "conversation" him and Brennan had that morning,

"It was okay. No case so I just did paperwork." He began getting changed into comfortable clothing. Hannah had gotten up and was going into the kitchen. Booth felt for his phone but couldn't find it.

"Hey babe? Can you grab my cell in my coat pocket?" She called back a yeah. As he settled his t shirt he heard Hannah call for him,

"Seeley, can you come here one moment?" Confused he made his way out of the bedroom. He saw her standing by the island holding a crumpled piece of paper,

"Seeley, what the hell is this?" She grew angry. He took the paper and read it. He quickly saw that it was the letter "Brennan" wrote to him. His mouth gaped open a little,

"Hannah, this is not what it looks like." She put her hands on her hips,

"Oh really? Because this looks like your partner is professing her love for you. I can't believe it!" He tried to calm her down,

"Hannah please let me explain-" She cut him off,

"Nope. This isn't happening. I cannot believe that bitch did this to us. I mean seriously is she so cold and alone that she has to try to steal my boyfriend?!" Booth's eyes widened in anger. No one talks about his Bones like that,

"Now wait a minute. She is not cold or alone. She is an amazing woman who deserves everything. How could you say that stuff about her?" She grew more angry,

"Why are you defending her? That ice queen is trying to ruin us how can you sit there and defend her? and I'm saying all of this stuff because its true." They stood face to face now,

"I'm defending her because she is my best friend. She is my family and I will not stand here and let you talk down about her." Her eyes widened,

"Are you serious right now? Seeley, she is trying to drive us apart! That soul-less bitch needs to go." He shook his head and began yelling,

"I don't think she's the one who needs to go." She took a step back at his implication.

"So you want me to leave?" He sighed and spoke,

"Are you making me choose between her and you?" She nodded. He took a deep breath and answered her previous question,

"Then yes. I refuse to be with someone who makes me choose and who will talk about my family in that way. Bones is the most amazing person in the world and would do anything for me. She greeted you with open arms even though it hurt her and this is how you view her? You don't even know the backstory of this whole thing. The fact that you jump to that conclusion of her tells me you are not who I thought you were. I'm leaving but when I return in an hour I want you completely gone." She tried to stop,

"Seeley-" He shrugged her off and left his apartment, leaving a devastated Hannah behind. He went to the founding fathers and ordered a drink, giving his now ex time to clear out of his apartment.

* * *

 **Not really a cliffhanger but thats** **Okay! I hope you enjoyed this chapter -J.A.**


	7. Chapter 7

**Hey guys! I'm glad you liked the last chapter. Here is chapter 7**

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Days flew by with no contact between the partners. Booth would text her here and there in hopes that she would answer. She never did. Her heart ached every time a notification would pop up and she would see his name. She was growing tired of being angry and hurt. She was coming up to wanting to talk to Booth and Angela and setting things right. That night after leaving the lab she made it her mission to talk to her friends. First, Booth.

Booth sat on his couch nursing a beer he had no intension of drinking. It had been almost a week since his blowup on Brennan and a few days since Hannah left. His life was spiraling out of control. All he kept thinking about was how much of an idiot he is and how he ruined his relationship with Brennan. He was jarred from his thoughts by a knock on the door. Booth opened his door and found his partner standing there. It had been a few days since he had seen her and he was glad that she was standing on his front doorstep,

"Bones." he gave her a smile in relief, she didn't return one,

"Hello Booth. May I come in?" He nodded and stepped out of the way to let her come inside. She stood in his living room taking in the scenery. "I uh, hope I'm not ruining yours and Hannah's evening." Booth rubbed his neck and spoke,

"Well, You see Bones. Hannah moved out a few days ago. We are no longer together." Booth saw something in his partners eyes but it was gone faster than it appeared. She walked around his apartment a little and found her way to his living room,

"Oh. I'm very sorry that things didn't work out for you. I uh *clears throat* I knew how happy you were with her." her words make them recall back to the hurtful words Booth had yelled to her just a week before. Booth shuffled uncomfortably,

"Uh yeah. It sucks but I don't think we were meant for each other." Brennan's eyes furrowed,

"But you said that you loved her, on many occasions." He nodded,

"Yeah I did but I don't think I was being honest when I was saying that." She shook her head,

"So… why did you yell that to me in front of everybody last week?" He was caught off guard by her statement. it seems like she was ready to talk about what happened.

"I was hurt Bones. I thought you wrote me the letter and it hurt me to see how distant and cold it was." She shook her head and looked at her feet,

"You should know me better than that Booth. You should have known I would never do something like that to you." He closed his eyes and nodded,

"I'm so sorry Bones. I knew you would never do something like that but..." he looked down at his feet,

"But?..." she prodded on. He sighed and spoke,

"I felt us pulling away from each other and when I read the letter I... I don't even know what I was thinking. I read it and I just got so mad. I should have known you would never do something like this." He dropped to his couch and put his head in his hands. They stood in complete silence, her standing by his coffee table and him on the couch. When he looked up he saw her reading a piece of paper. He realized that she was reading "her" letter to him,

"Is this the letter Angela wrote?" She asked but already knew the answer,

"Yes." She nodded,

"Wow, she wrote word for word." He heard her mumble to no one. He looked puzzled,

"What do you mean?" She looked up and hadn't realized she said that out loud. Instead of lying she decided to be honest about her feelings for him,

"The night before all of this I was with Angela, we were talking about.. us." She looked down at her feet in slight embarrassment, "everything I said she wrote down in this letter." He was somewhat shocked. He thought this letter was just Angela being an instigator but he realized that Brennan felt that way about him.. or she used to before he messed everything up. He saw wheels turning in her head,

"Is this why you and Hannah broke up?" She asked. He respected the honesty they had going so he nodded his head,

"She found the letter in my jacket pocket. We fought and she left." Brennan nodded.

"I'm sorry." She said quietly. He got up and stood in front of her,

"Don't be sorry. This was not your fault. Hannah and I... we weren't that great together. She wasn't a settler. She wanted to go and used this as an out. I'm not upset about it though." Brennan nodded.

"You're not upset about this? If you're not upset about this than why did you humiliate me in an effort to prove to me that you are happy and you love Hannah?" He bowed his head in shame,

"Bones. I'm so sorry about what I said. I didn't mean any of it." She looked confused and angry,

"You told me that I make things cold and rational. You said that my words meant nothing to you and now that I'm reading what Angela wrote it's clear that what I said doesn't matter. You moved on. I didn't doubt that at all. If I never gave you the impression that I doubted that you were happy and you moved on why did you come into the lab and completely rip me apart in front of my whole staff? Why did you feel like humiliating me in front of everyone? You read that letter. You thought it was from me. So all of those hurtful words you threw at me you meant." She stood there with her arms crossed and anger flowing through her body. Booth, trying to control his emotions, spoke,

"Bones. I said all of those things because I wanted to hurt you like how the letter hurt me. I was so shocked when I read this and so angry. I immediately came to the lab and just started yelling. I didn't even realized what I said until I had a moment to cool down. I need you to believe me. I didn't mean anything I said. Your words mean everything to me. You're not cold and rational. I was so unhappy with Hannah and I couldn't move on." That last part caught her off guard. She looked at him with wide eyes and spoke,

"You couldn't move on?" He nodded "I never wanted you to." They looked into each others eyes for a while, not daring to say a word. Booth was the first to speak,

"So... what happens now?" Tears welled up in her eyes,

"You just broke up with Hannah and I'm still very hurt over your words, even though you said you didn't mean them. We can't do this right now Booth. We both need time to get into the right place so we don't mess things up." Booth understood her logic and agreed with her. She saw him nod as she made her way to the door. Before opening it she turned towards him,

"We need some time Booth." He nodded,

"Time and space?" Her asked nervously. She looked into his eyes and spoke,

"No. Just time." He sighed in relief in his head. He nodded and they both spoke their goodbyes. He closed the door behind her and leaned up against it. The talk didn't end how he wanted it to but he was so happy that things were going to get better for them.

* * *

Brennan walked up to the door and knocked softly. She hoped she wasn't disturbing Angela and Hodgins' night but she knew in the back of her mind Angela would be thrilled to speak to her. She stood there nervous and waited to hear the soft click of the lot and the door being opened. Hogins stood there in shock,

"Dr B. please come in." She nodded and walked into the house, "Angie is upstairs." Brennan nodded once more,

"How is she?" Hodgins shrugged,

"She's Okay. She's a bit upset with herself but other than that she's good." Brennan nodded. She followed him up the stairs to the bedroom. Hodgins left her at the closed door so the friends can speak privately. Brennan took a deep breath and knocked. Hearing a soft "hodgins why are you knocking?" Brennan chuckled to herself and made her way into the room. Angela was surprised to see her best friend standing there.

"Hi Angela." Brennan said softly.

"Bren. Hi. Please sit." Brennan hesitantly made her way to the bed and took a seat across from her friend,

"I hope I'm not bothering you." Angela shook her head quickly,

"You're not bothering me at all! How are you?" Brennan looked at her hands in her lap and shrugged,

"I'm Okay. I'm here to talk to you." Angela nodded and braced herself. Brennan took a deep breath and spoke, "Angela, What you did was wrong. I know you meant well, you always do but this was taking it way too far. I know you want me to be happy but you have to let me do it myself. You have to stop getting in the middle of my happiness." Tears spilled over Angela's eyes when hearing her friends words.

"I'm so sorry Bren. I never meant to hurt you." Echoing Booth's words. Brennan sighed and spoke,

"I know your sorry." Acceptance wasn't in Brennan's mind at the moment but she didn't doubt she would get there soon. She hated what Angela said next,

"I'm so sorry. Will you accept my apology?" Brennan took a deep breath and spoke,

"In time I will. I cannot say that I accept your apology right now because I do not believe I do. For years you've been trying to get Booth and I together. Your little stunts you've played with us were harmless but this one was too much. How did you even come up with this idea? You're my best friend, you should have known that I would never do that to Booth." Brennan was trying to control her anger. Angela hung her head in shame,

"I don't even remember why I did it in all honesty. It seemed like a good idea at the time. I didn't expect Booth to react that way. I'm sorry I provoked it." All Brennan could do was nod. The pair sat for a few moments in silence before Brennan got up to go home. She felt a lot better but not 100%. She said her goodbyes and was about to leave when Angela stopped her,

"Are we Okay Bren?" she asked fearfully. Brennan sighed,

"We will be." Brennan left after that and went straight home.

* * *

 **I hope you enjoyed this chapter! There is probably one or two more chapters in this story! See ya on the flipside guys. -J.A.**


	8. Chapter 8

**Hey guys! So, this is the end. I hope you guys enjoyed this story! I've been on an angst kick for a while now, I need to start writing fluff in the middle. Here is the final chapter**

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 _A few months later... (6x22 The Hole in the Heart)_

Brennan laid on Booth's couch, too caught in her thoughts to go to sleep. Her intern was dead. Vincent was a good kid and he didn't deserve to die. As she was thinking of her intern she hounded on one thought,

 _It was supposed to be Booth. He was supposed to get shot._ That thought kept circling in her mind. Booth was supposed to answer the phone, he was supposed to be shot, he would be dead right now. They both knew that Broadsky was an amazing shot; if he wanted to kill Booth he would have. Brennan couldn't wrap her head around that thought. It was really close; if Booth died she would have too.

The realization made her eyes shoot open. She didn't want to live without him. He meant so much to her. For the last few moths he has been trying so hard to gain her trust back. She noticed his efforts and it has softened her anger towards him. Tonight though, she realized that life is too short to stay angry. She was ready to let go and give herself fully to Booth.

Brennan continued on thinking about Vincent and what he said before he died, she thought of everything that has happened in the past 24 hours. After willing herself to move she walked slowly to Booth's room. She creaked open the door and noticed him jump for his gun...

 _Later..._

Booth held his grieving partner in comfort. It was a devastating time for all of them. All he could think about was that it was supposed to be him. He should have died not Vincent. He felt her tears subside as she calmed down. He felt the tears soak through his shirt but he didn't care; he held her tighter and rubbed her back,

"Booth." He heard her say faintly, "I forgive you." His heart stopped. The three words he has been working so hard to hear. He sighed in relief and spoke,

"I'm glad to hear that." She looked at him with her chin resting on his chest, red eyes and tears still coming out,

"After tonight I realized that life is short. Staying angry is not a smart idea. I forgive you Booth." He gave her a small smile. "I also realized that life is too short to hold back my feelings." Before Booth could ask her what she meant she reached up and placed a soft kiss on his lips. He was stunned by the gesture but quickly got out of that. He tightened his hold on her and pulled her in more. She deepened the kiss. When they broke apart Booth could only ask one question,

"Are you sure Bones?" she gave him a small smile,

"I'm ready Booth. If you are as well I would love to continue forward in life with you." All he could do was nod. He pulled her into another kiss to seal the deal.

The next morning they laid in bed holding one another for a while before they had to leave. They didnt know what the day would bring them but they were ready. Before leaving Brennan's apartment she pulled him into a deep kiss. Silently wishing him good luck and that she loves him.

 _Later.._

"Away!" Angela yelled at her husband. Hodgins scurried away to go see Cam. Angela threw her hands down onto the table,

"Bren. Oh my god finally! What happened?" She was so giddy Brennan feared she would make herself go into labor,

"I was upset last night. He held me as I cried. While I was sitting there I realized that life is too short to stay angry. We decided to go forward and start a life together. Which is why I'm glad you're here." Angela looked confused,

"I forgive you Angela. I know you were only looking out for me and staying mad for so long is a waste of time." Angela bursted into tears and enveloped her friend into a hug. The woman held each other for a while before getting back to the task at hand. Catching Jacob Broadsky.

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 **Well, thats it! I hope you enjoyed the ending. I didn't want to stray away from the canon story for the ending. Check out my page for more Bones stories. See ya on the flipside guys! -J.A.**


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